All Methods Instance Methods Abstract Methods
Modifier and Type |
Method |
Description |
Integer |
countLinks(Gene gene,
BioAssaySet ee) |
|
Map<Gene,Integer> |
countOldLinks(Collection<Gene> genes) |
|
void |
createOrUpdate(BioAssaySet bioAssaySet,
List<NonPersistentNonOrderedCoexpLink> p2plinks,
LinkCreator c,
Set<Gene> genesTested) |
|
void |
deleteLinks(Taxon taxon,
BioAssaySet experiment) |
|
List<CoexpressionValueObject> |
findCoexpressionRelationships(Gene gene,
Collection<Long> bas,
int maxResults,
boolean quick) |
Find coexpression links for a gene that are common to all the given datasets.
|
Map<Long,List<CoexpressionValueObject>> |
findCoexpressionRelationships(Taxon taxon,
Collection<Long> genes,
Collection<Long> bas,
int maxResults,
boolean quick) |
Find coexpression links for the genes that are common to all the given datasets, so stringency = bas.size().
|
Map<Long,List<CoexpressionValueObject>> |
findCoexpressionRelationships(Taxon t,
Collection<Long> genes,
Collection<Long> bas,
int stringency,
int maxResults,
boolean quick) |
|
Map<Long,List<CoexpressionValueObject>> |
findInterCoexpressionRelationships(Taxon taxon,
Collection<Long> genes,
Collection<Long> bas,
int stringency,
boolean quick) |
Return coexpression relationships among the given genes, limited to the given data sets.
|
Collection<CoexpressionValueObject> |
getCoexpression(Taxon taxon,
BioAssaySet experiment,
boolean quick) |
|
boolean |
hasLinks(Taxon taxon,
BioAssaySet ee) |
|
Map<SupportDetails,Gene2GeneCoexpression> |
initializeFromOldData(Gene gene,
Map<Long,Gene> geneIdMap,
Map<NonPersistentNonOrderedCoexpLink,SupportDetails> linksSoFar,
Set<Long> skipGenes) |
|
int |
queryAndCache(Gene gene) |
|
GeneCoexpressionNodeDegreeValueObject |
updateNodeDegree(Gene gene,
GeneCoexpressionNodeDegree nd) |
This is a maintenance method.
|
void |
updateRelativeNodeDegrees(Map<Long,List<Double>> relRanksPerGenePos,
Map<Long,List<Double>> relRanksPerGeneNeg) |
|